Prediction and verification of mouse tRNA gene families

Background: Transfer RNA (tRNA) gene predictions are complicated by challenges such as structural variation, limited sequence conservation and the presence of highly reiterated short interspersed sequences (SINEs) that originally derived from tRNA genes or tRNA-like transcription units. Annotation of "tRNA genes" in sequenced genomes generally have not been accompanied by experimental verification of the expression status of predicted sequences. Results: To address this for mouse tRNA genes, we have employed two programs, tRNAScan-SE and ARAGORN, to predict the tRNA genes in the nuclear genome, resulting in diverse but overlapping predicted gene sets. From these, we removed known SINE repeats and sorted the genes into predicted families and single-copy genes. In particular, four families of intron-containing tRNA genes were predicted for the first time in mouse, with introns in positions and structures similar to the well characterized intron-containing tRNA genes in yeast. We verified the expression of the predicted tRNA genes by microarray analysis. We then confirmed the expression of appropriately sized RNA for the four intron-containing tRNA gene families, as well as the other 30 tRNA gene families creating an index of expression-verified mouse tRNAs. Conclusions: These confirmed tRNA genes represent all anti-codons and all known mammalian tRNA structural groups, as well as a variety of predicted "rogue" tRNA genes within families with altered anticodon identities.